AML datasets

Mouse datasets

Note: Validation mice also available via Haemdata/Ondrive. See X for more details.

First, we need to setup the pin-board and download the mouse datasets.

library(haemdata)
use_pinboard("onedrive")

all_mice <- get_pin("mmu_mrna_all_mice_GENCODEm28_HLT_qc.rds")
metadata_mmu <- get_pin("metadata_mmu.csv")

2016 mice

se <- subset(all_mice,
    select = grepl("2016", SummarizedExperiment::colData(all_mice)$batch)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

metadata_mmu |>
plot_cohort_survival("AML.mRNA.2016")

2018 mice

se <- subset(all_mice,
    select = grepl("AML.mRNA.2018.all_samples", SummarizedExperiment::colData(all_mice)$cohort)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

metadata_mmu |>
plot_cohort_survival("AML.mRNA.2018")

Radiation mice

se <- subset(all_mice,
    select = grepl("AML.mRNA.2020", SummarizedExperiment::colData(all_mice)$cohort)
)
se <- subset(se,
    select = grepl("PBMC", SummarizedExperiment::colData(se)$tissue)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

metadata_mmu |>
plot_cohort_survival("AML.mRNA.2020")

Chemo mice

se <- subset(all_mice,
    select = grepl("RxGroup", SummarizedExperiment::colData(all_mice)$cohort)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

metadata_mmu |>
plot_cohort_survival("RxGroup")

scRNAseq mice 2022

se <- subset(all_mice,
    select = grepl("AML.scRNAseq.2022", SummarizedExperiment::colData(all_mice)$cohort)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

Bone marrow

se <- subset(all_mice,
    select = ("BM" == SummarizedExperiment::colData(all_mice)$tissue)
)
se <- subset(se,
    select = grepl("AML", SummarizedExperiment::colData(se)$cohort)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

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